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• Molecular correlates for HPV-negative head and neck cancer engraftment prognosticate patient outcomes

  Head and neck squamous cell carcinoma (HNSCC) tumors were sampled from 88 patients. Samples were implanted subcutaenously into the flank of NOD/SCID/IL2R-/- mice. Mice were then monitored weekly for tumor growth and the time of initial palpation was recorded. Mice were euthanized when tumors reached 15 mm in diameter or after 6 months. If no tumor formed by 6 months, the patient tumor was defined as Non-engrafter (N). RNA-seq was performed on all primary tumor samples and successfully engrafted patient-derived xenograft (PDX) samples.

  Study EGAS50000000714

• Comparison of single/pooled CTCs and bulk exome sequencing

  Single cell technologies allow the interrogation of tumor heterogeneity, providing insights into tumor evolution and treatment resistance. To better understand whether circulating tumor cells (CTCs) could complement metastatic biopsies for tumor genomic profiling, we characterized 11 single CTCs and 10 pooled CTC samples at the mutational and copy number aberration (CNA) levels, and compared these results with matched synchronous tumor biopsies from 3 metastatic breast cancer patients with triple-negative (TNBC), HER2-positive and estrogen receptor-positive (ER+) tumors. Similar CNA profiles and the same patient-specific driver mutations were found in bulk tissue and CTCs for the HER2-positive and TNBC tumors, whereas different CNA profiles and driver mutations were identified for the ER+ tumor, which presented two distinct clones in CTCs defined by mutations in ESR1 Y537N and TP53, respectively. Furthermore, de novo mutational signatures derived from CTCs described patient-specific biological processes. These data suggest that tumor tissue and CTCs provide complementary clinically relevant information to map tumor heterogeneity and tumor evolution.

  Dataset EGAD00001009052

• Human Responses to Influenza Vaccination

  The data consist of the DNA sequences of antibody gene rearrangements from peripheral blood human B cells of subjects vaccinated with trivalent seasonal influenza or monovalent pandemic H1N1 vaccine. Multiple replicate libraries of immunoglobulin heavy chain gene rearrangements were prepared from each subject for each time point.

  Study phs000760

• RNAseq of Sjögren's Syndrome and Healthy Volunteers' Salivary Glands

  Mechanistic genetic and inflammatory endpoints were studied to gain insight into the molecular mechanisms of Sjögren's syndrome. Transcriptomic studies allowed the exploration of molecular alterations that might cause or influence the studied salivary gland pathology and potentially elucidate druggable pathways for intervention.

  Study phs001842

• Analysis of transcriptomic landscape of iPSC-derived neurons in Williams Syndrome

  To analyse the transcriptomic changes in iPSC-derived neuronal cells derived from individuals with Williams syndrome vs. controls at different stages of neuronal maturation. This was done to better understand how the deletion responsible for WS alters neuronal development thereby resulting in the characteristic WS phenotype

  Study EGAS50000001214

• WES of tumor samples from patients with renal medullary carcinoma (RMC)

  The dataset, in .bam file format, consists of whole exome sequencing (WES) data of tumors from patients (n=24) with Renal Medullary Carcinoma (RMC), generated using Illumina NovaSeq 6000 sequencing technology. DNA was extracted from FFPE solid tumor samples using the AllPrep DNA FFPE Kit (Qiagen, CA). Libraries from FFPE tissue were prepared with the SureSelect XT HS2 DNA Kit (Agilent, CA) for exome capture. The All Exon V7 exome probe set (Agilent, CA) was used for hybridization and capture of DNA.

  Dataset EGAD50000001822

• RNA-seq data for proximal and distal human LHBT UZH (CH)

  This dataset contains bulk RNA-seq data from 15 patients who underwent rotator cuff repair surgery, yielding paired proximal and distal samples of the long head of the biceps tendon (30 samples total). The submission includes 90 files, consisting of R1 and R2 FASTQ files for each sample as well asprocessed .TXT files containing gene-level counts generated after genome alignment. Raw sequencing reads were generated on an Illumina platform, aligned to the human reference genome GRCh38.p13, and quantified at the gene level.

  Dataset EGAD50000002095

• Fragmentomics analyses of urinary cfDNA for urologic cancers

  This dataset contains sequencing data of human urinary cell-free DNA. Whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) was performed after DNA extraction from the urine samples. All samples were pair-end sequencing on Illumina system and were aligned to human genome GRCh37 (hg19). WGS and WGBS reads were aligned by SOAP2 and Methyl-Pipe, respectively. The dataset includes samples from healthy subjects, haematuria (non-cancer), and patients of bladder, kidney, or prostate cancer. Pair-end FASTQ files were provided for all the samples mentioned above.

  Dataset EGAD50000002068

• RNA-sequencing of 82 pleural mesothelioma samples

  The dataset contains RNA-sequencing data (bam files) for 82 pleural mesothelioma samples. All the samples were sequenced on an Illumina NovaSeq 600 sequencer in paired-end mode, generating 100 nt length reads, to obtain an average of 60 million clusters for RNA. Demultiplexing was performed using Illumina bcl2fastq2. Fastq quality was assessed using fastQC (v. 0.11.8) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and low-quality reads were discarded. Sequence reads were aligned to Human reference genome (UCSC genome assembly GRCh38/hg38) using STAR (v. 2.7.0b).

  Dataset EGAD50000002131

• Gene expression matrix for Smart-seq2 data of peripheral blood B cells

  The dataset contains scRNA-seq gene expression matrix (csv file) and metadata (csv file) after quality control filtering for data generated with the Smart-seq2 protocol. Transcript expression was quantified with Salmon v0.11.3 using cDNA sequences from GRCh38.94 and k-mer length 25, and was aggregated to gene level and transcript-length-corrected using tximport v1.8.0. The dataset comprises IgA+ transglutaminase 2-specific and other IgA+ B cells from the peripheral blood of 355 cells from two untreated celiac disease patients.

  Dataset EGAD50000000338